Starting phenix.real_space_refine on Sun Mar 10 19:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/03_2024/7f9w_31499.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2654 2.51 5 N 713 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4217 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 bond proxies already assigned to first conformer: 863 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1669 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 25 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 25 " occ=0.50 Time building chain proxies: 3.04, per 1000 atoms: 0.72 Number of scatterers: 4217 At special positions: 0 Unit cell: (64.26, 64.8, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 828 8.00 N 713 7.00 C 2654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 910.0 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.834A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.700A pdb=" N LEU C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.727A pdb=" N LYS C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.705A pdb=" N GLN A 130 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 145 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.612A pdb=" N TYR A 20 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.878A pdb=" N LEU A 45 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.136A pdb=" N LEU C 11 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 90 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 91 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 41 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.532A pdb=" N THR C 78 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.811A pdb=" N LYS C 36 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.542A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 138 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 185 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.827A pdb=" N TRP C 154 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 198 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.571A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 33 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 162 through 163 142 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1349 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4322 Sorted by residual: bond pdb=" CB PRO C 147 " pdb=" CG PRO C 147 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C PHE C 104 " pdb=" N GLY C 105 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 ... (remaining 4317 not shown) Histogram of bond angle deviations from ideal: 96.99 - 104.41: 90 104.41 - 111.82: 2154 111.82 - 119.24: 1319 119.24 - 126.66: 2234 126.66 - 134.08: 78 Bond angle restraints: 5875 Sorted by residual: angle pdb=" C GLN C 96 " pdb=" N TYR C 97 " pdb=" CA TYR C 97 " ideal model delta sigma weight residual 122.65 116.83 5.82 1.66e+00 3.63e-01 1.23e+01 angle pdb=" N TYR C 146 " pdb=" CA TYR C 146 " pdb=" C TYR C 146 " ideal model delta sigma weight residual 108.82 103.55 5.27 1.69e+00 3.50e-01 9.74e+00 angle pdb=" C GLU A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C HIS B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta sigma weight residual 120.09 123.62 -3.53 1.25e+00 6.40e-01 7.99e+00 angle pdb=" C LEU B 133 " pdb=" N ALA B 134 " pdb=" CA ALA B 134 " ideal model delta sigma weight residual 120.60 124.34 -3.74 1.53e+00 4.27e-01 5.99e+00 ... (remaining 5870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2385 16.30 - 32.61: 150 32.61 - 48.91: 40 48.91 - 65.21: 3 65.21 - 81.52: 13 Dihedral angle restraints: 2591 sinusoidal: 1004 harmonic: 1587 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual 93.00 159.24 -66.24 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 143.75 -50.75 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.054: 182 0.054 - 0.081: 59 0.081 - 0.107: 43 0.107 - 0.134: 14 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR C 97 " pdb=" N TYR C 97 " pdb=" C TYR C 97 " pdb=" CB TYR C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 643 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 56 " -0.015 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP C 56 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 56 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 56 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 56 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 56 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 56 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 134 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 135 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 155 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 156 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 85 2.67 - 3.23: 3920 3.23 - 3.79: 6053 3.79 - 4.34: 8034 4.34 - 4.90: 13974 Nonbonded interactions: 32066 Sorted by model distance: nonbonded pdb=" OE2 GLU C 111 " pdb=" NE2 GLN C 172 " model vdw 2.114 2.520 nonbonded pdb=" OG SER B 212 " pdb=" OG1 THR B 214 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR A 47 " pdb=" O SER A 54 " model vdw 2.212 2.440 nonbonded pdb=" O SER C 83 " pdb=" NE2 GLN C 85 " model vdw 2.221 2.520 nonbonded pdb=" N GLY A 141 " pdb=" OG SER B 104 " model vdw 2.252 2.520 ... (remaining 32061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.680 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4322 Z= 0.334 Angle : 0.677 5.819 5875 Z= 0.371 Chirality : 0.043 0.134 646 Planarity : 0.005 0.053 753 Dihedral : 12.990 81.517 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.63 % Allowed : 0.21 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.38), residues: 539 helix: 0.20 (1.48), residues: 13 sheet: 0.41 (0.37), residues: 234 loop : 0.05 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 56 HIS 0.002 0.000 HIS B 173 PHE 0.014 0.002 PHE C 145 TYR 0.024 0.002 TYR C 97 ARG 0.004 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.454 Fit side-chains REVERT: A 18 MET cc_start: 0.8747 (mmp) cc_final: 0.8477 (mmt) REVERT: A 26 LEU cc_start: 0.6275 (tt) cc_final: 0.5996 (tt) REVERT: A 45 LEU cc_start: 0.8311 (tp) cc_final: 0.8091 (tt) REVERT: A 106 GLU cc_start: 0.8553 (pp20) cc_final: 0.8322 (pp20) REVERT: A 155 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8381 (tmt170) REVERT: A 160 GLN cc_start: 0.8279 (mm110) cc_final: 0.8026 (mm110) REVERT: C 1 ASP cc_start: 0.8395 (p0) cc_final: 0.8182 (p0) REVERT: C 128 ASP cc_start: 0.8519 (p0) cc_final: 0.8087 (p0) REVERT: C 153 GLN cc_start: 0.7248 (mp10) cc_final: 0.6837 (mp10) REVERT: B 59 ASP cc_start: 0.7667 (t0) cc_final: 0.7417 (t0) REVERT: B 73 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1858 time to fit residues: 21.4814 Evaluate side-chains 83 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4322 Z= 0.242 Angle : 0.621 6.571 5875 Z= 0.323 Chirality : 0.043 0.154 646 Planarity : 0.005 0.042 753 Dihedral : 4.741 21.316 589 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.63 % Allowed : 6.13 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.39), residues: 539 helix: 0.91 (1.53), residues: 13 sheet: 0.52 (0.36), residues: 245 loop : 0.24 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 56 HIS 0.002 0.001 HIS A 139 PHE 0.018 0.002 PHE B 64 TYR 0.021 0.002 TYR C 97 ARG 0.005 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.509 Fit side-chains REVERT: A 18 MET cc_start: 0.8729 (mmp) cc_final: 0.8454 (mmt) REVERT: A 126 MET cc_start: 0.8182 (ppp) cc_final: 0.7848 (ppp) REVERT: A 155 ARG cc_start: 0.8670 (ptm-80) cc_final: 0.8429 (tmt170) REVERT: A 160 GLN cc_start: 0.8305 (mm110) cc_final: 0.7924 (mm110) REVERT: C 1 ASP cc_start: 0.8359 (p0) cc_final: 0.8087 (p0) REVERT: C 17 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 176 ASP cc_start: 0.8151 (m-30) cc_final: 0.7926 (t70) REVERT: B 59 ASP cc_start: 0.7531 (t0) cc_final: 0.7247 (t0) REVERT: B 73 ASP cc_start: 0.8338 (t0) cc_final: 0.8115 (t0) REVERT: B 100 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7727 (mtp-110) outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.1915 time to fit residues: 19.8341 Evaluate side-chains 78 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4322 Z= 0.246 Angle : 0.590 5.399 5875 Z= 0.310 Chirality : 0.043 0.156 646 Planarity : 0.004 0.035 753 Dihedral : 4.602 20.707 589 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.11 % Allowed : 8.88 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.39), residues: 539 helix: 1.09 (1.56), residues: 13 sheet: 0.54 (0.36), residues: 247 loop : 0.26 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.002 0.000 HIS B 209 PHE 0.012 0.001 PHE B 64 TYR 0.022 0.002 TYR C 97 ARG 0.004 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.509 Fit side-chains REVERT: A 18 MET cc_start: 0.8719 (mmp) cc_final: 0.8443 (mmt) REVERT: A 160 GLN cc_start: 0.8308 (mm110) cc_final: 0.7912 (mm110) REVERT: C 1 ASP cc_start: 0.8342 (p0) cc_final: 0.8055 (p0) REVERT: C 17 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 128 ASP cc_start: 0.8868 (p0) cc_final: 0.8636 (p0) REVERT: C 176 ASP cc_start: 0.8194 (m-30) cc_final: 0.7986 (t70) REVERT: B 59 ASP cc_start: 0.7561 (t0) cc_final: 0.7296 (t0) REVERT: B 73 ASP cc_start: 0.8376 (t0) cc_final: 0.8111 (t0) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.1729 time to fit residues: 18.5315 Evaluate side-chains 83 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4322 Z= 0.385 Angle : 0.637 6.433 5875 Z= 0.336 Chirality : 0.044 0.159 646 Planarity : 0.004 0.035 753 Dihedral : 4.784 20.693 589 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.33 % Allowed : 11.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.38), residues: 539 helix: 0.95 (1.46), residues: 13 sheet: 0.48 (0.36), residues: 243 loop : 0.03 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 154 HIS 0.002 0.000 HIS B 173 PHE 0.017 0.002 PHE B 64 TYR 0.032 0.002 TYR C 97 ARG 0.005 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.505 Fit side-chains REVERT: A 18 MET cc_start: 0.8743 (mmp) cc_final: 0.8416 (mmt) REVERT: A 160 GLN cc_start: 0.8321 (mm110) cc_final: 0.7889 (mm110) REVERT: C 1 ASP cc_start: 0.8372 (p0) cc_final: 0.8013 (p0) REVERT: C 17 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7978 (tm-30) REVERT: B 59 ASP cc_start: 0.7588 (t0) cc_final: 0.7298 (t0) REVERT: B 73 ASP cc_start: 0.8372 (t0) cc_final: 0.8107 (t0) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.1867 time to fit residues: 20.2594 Evaluate side-chains 89 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4322 Z= 0.171 Angle : 0.561 7.738 5875 Z= 0.289 Chirality : 0.042 0.153 646 Planarity : 0.004 0.030 753 Dihedral : 4.454 20.696 589 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.75 % Allowed : 11.84 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 539 helix: 1.26 (1.51), residues: 13 sheet: 0.60 (0.35), residues: 245 loop : 0.12 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.001 0.000 HIS A 103 PHE 0.007 0.001 PHE B 64 TYR 0.013 0.001 TYR C 97 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8700 (mmp) cc_final: 0.8426 (mmt) REVERT: A 160 GLN cc_start: 0.8303 (mm110) cc_final: 0.7890 (mm110) REVERT: C 1 ASP cc_start: 0.8290 (p0) cc_final: 0.7995 (p0) REVERT: C 17 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 176 ASP cc_start: 0.8056 (m-30) cc_final: 0.7783 (t70) REVERT: B 59 ASP cc_start: 0.7560 (t0) cc_final: 0.7302 (t0) REVERT: B 73 ASP cc_start: 0.8349 (t0) cc_final: 0.8068 (t0) outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 0.1572 time to fit residues: 18.2173 Evaluate side-chains 87 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4322 Z= 0.169 Angle : 0.545 5.761 5875 Z= 0.283 Chirality : 0.042 0.145 646 Planarity : 0.004 0.032 753 Dihedral : 4.307 19.963 589 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.54 % Allowed : 12.68 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.38), residues: 539 helix: 1.28 (1.48), residues: 13 sheet: 0.66 (0.35), residues: 245 loop : 0.11 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.012 0.001 PHE A 15 TYR 0.013 0.001 TYR C 97 ARG 0.002 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8688 (mmp) cc_final: 0.8396 (mmt) REVERT: A 157 THR cc_start: 0.8411 (p) cc_final: 0.8075 (p) REVERT: A 160 GLN cc_start: 0.8294 (mm110) cc_final: 0.7892 (mm110) REVERT: C 1 ASP cc_start: 0.8216 (p0) cc_final: 0.7956 (p0) REVERT: C 17 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7987 (tm-30) REVERT: C 176 ASP cc_start: 0.8046 (m-30) cc_final: 0.7780 (t70) REVERT: B 59 ASP cc_start: 0.7554 (t0) cc_final: 0.7280 (t0) REVERT: B 73 ASP cc_start: 0.8310 (t0) cc_final: 0.7998 (t0) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1902 time to fit residues: 22.5434 Evaluate side-chains 89 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4322 Z= 0.248 Angle : 0.594 7.866 5875 Z= 0.302 Chirality : 0.043 0.148 646 Planarity : 0.004 0.033 753 Dihedral : 4.385 20.379 589 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.17 % Allowed : 14.38 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 539 helix: 1.23 (1.48), residues: 13 sheet: 0.64 (0.36), residues: 245 loop : 0.07 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.011 0.001 PHE A 15 TYR 0.022 0.002 TYR C 97 ARG 0.007 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.491 Fit side-chains REVERT: A 18 MET cc_start: 0.8709 (mmp) cc_final: 0.8390 (mmt) REVERT: A 111 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8859 (mp0) REVERT: A 160 GLN cc_start: 0.8306 (mm110) cc_final: 0.7941 (mm110) REVERT: C 1 ASP cc_start: 0.8283 (p0) cc_final: 0.7971 (p0) REVERT: C 17 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 129 GLU cc_start: 0.8688 (mp0) cc_final: 0.8367 (mp0) REVERT: C 176 ASP cc_start: 0.8088 (m-30) cc_final: 0.7844 (t70) REVERT: B 59 ASP cc_start: 0.7578 (t0) cc_final: 0.7314 (t0) REVERT: B 73 ASP cc_start: 0.8310 (t0) cc_final: 0.7991 (t0) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.1806 time to fit residues: 20.8533 Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4322 Z= 0.227 Angle : 0.581 7.291 5875 Z= 0.296 Chirality : 0.042 0.148 646 Planarity : 0.004 0.032 753 Dihedral : 4.370 20.212 589 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.96 % Allowed : 13.95 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.38), residues: 539 helix: 1.10 (1.43), residues: 13 sheet: 0.57 (0.35), residues: 245 loop : 0.06 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.012 0.001 PHE A 15 TYR 0.020 0.001 TYR C 97 ARG 0.007 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.519 Fit side-chains REVERT: A 18 MET cc_start: 0.8713 (mmp) cc_final: 0.8379 (mmt) REVERT: A 160 GLN cc_start: 0.8288 (mm110) cc_final: 0.7916 (mm110) REVERT: C 1 ASP cc_start: 0.8296 (p0) cc_final: 0.7981 (p0) REVERT: C 17 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 129 GLU cc_start: 0.8644 (mp0) cc_final: 0.8345 (mp0) REVERT: C 176 ASP cc_start: 0.8092 (m-30) cc_final: 0.7842 (t70) REVERT: B 59 ASP cc_start: 0.7577 (t0) cc_final: 0.7316 (t0) REVERT: B 73 ASP cc_start: 0.8307 (t0) cc_final: 0.7987 (t0) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1705 time to fit residues: 19.7099 Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4322 Z= 0.185 Angle : 0.589 9.053 5875 Z= 0.294 Chirality : 0.042 0.146 646 Planarity : 0.004 0.031 753 Dihedral : 4.276 19.844 589 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.38 % Allowed : 14.59 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.38), residues: 539 helix: 1.10 (1.44), residues: 13 sheet: 0.59 (0.35), residues: 245 loop : 0.08 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 154 HIS 0.001 0.000 HIS C 195 PHE 0.012 0.001 PHE A 15 TYR 0.015 0.001 TYR C 97 ARG 0.007 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.498 Fit side-chains REVERT: A 18 MET cc_start: 0.8701 (mmp) cc_final: 0.8379 (mmt) REVERT: A 160 GLN cc_start: 0.8257 (mm110) cc_final: 0.7879 (mm110) REVERT: C 1 ASP cc_start: 0.8272 (p0) cc_final: 0.7985 (p0) REVERT: C 17 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 129 GLU cc_start: 0.8595 (mp0) cc_final: 0.8317 (mp0) REVERT: C 176 ASP cc_start: 0.8062 (m-30) cc_final: 0.7796 (t0) REVERT: B 59 ASP cc_start: 0.7563 (t0) cc_final: 0.7303 (t0) REVERT: B 73 ASP cc_start: 0.8285 (t0) cc_final: 0.7960 (t0) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.1648 time to fit residues: 18.9090 Evaluate side-chains 96 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 12 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4322 Z= 0.149 Angle : 0.577 8.985 5875 Z= 0.288 Chirality : 0.041 0.142 646 Planarity : 0.004 0.030 753 Dihedral : 4.115 19.777 589 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.96 % Allowed : 15.01 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 539 helix: 1.16 (1.45), residues: 13 sheet: 0.59 (0.35), residues: 246 loop : 0.13 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.002 0.000 HIS C 195 PHE 0.012 0.001 PHE A 15 TYR 0.010 0.001 TYR C 55 ARG 0.007 0.001 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8661 (mmp) cc_final: 0.8363 (mmt) REVERT: A 160 GLN cc_start: 0.8245 (mm110) cc_final: 0.7886 (mm110) REVERT: C 1 ASP cc_start: 0.8171 (p0) cc_final: 0.7927 (p0) REVERT: C 17 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 129 GLU cc_start: 0.8563 (mp0) cc_final: 0.8319 (mp0) REVERT: C 176 ASP cc_start: 0.7985 (m-30) cc_final: 0.7661 (t70) REVERT: B 59 ASP cc_start: 0.7542 (t0) cc_final: 0.7264 (t0) REVERT: B 73 ASP cc_start: 0.8263 (t0) cc_final: 0.7957 (t0) outliers start: 12 outliers final: 9 residues processed: 93 average time/residue: 0.1660 time to fit residues: 19.4019 Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.087497 restraints weight = 20949.145| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 5.87 r_work: 0.3017 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4322 Z= 0.330 Angle : 0.656 10.237 5875 Z= 0.329 Chirality : 0.043 0.148 646 Planarity : 0.004 0.043 753 Dihedral : 4.407 18.367 589 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.75 % Allowed : 15.64 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.38), residues: 539 helix: 0.96 (1.40), residues: 13 sheet: 0.49 (0.35), residues: 244 loop : -0.03 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 154 HIS 0.002 0.000 HIS A 151 PHE 0.012 0.001 PHE A 15 TYR 0.028 0.002 TYR C 97 ARG 0.008 0.001 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.52 seconds wall clock time: 27 minutes 7.28 seconds (1627.28 seconds total)